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- EMDB-36641: BJOX2000.664 trimer in complex with Fab fragment of broadly neutr... -

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Basic information

Entry
Database: EMDB / ID: EMD-36641
TitleBJOX2000.664 trimer in complex with Fab fragment of broadly neutralizing HIV antibody PGT145
Map data
Sample
  • Complex: BJOX2000.664 trimer in complex with broadly neutralizing HIV antibody PGT145
    • Protein or peptide: gp120 protein of HIV Envelope trimerEnvelope glycoprotein GP120
    • Protein or peptide: gp41 protein of HIV Envelope trimer
    • Protein or peptide: PGT145 antibody fragment, heavy chain
    • Protein or peptide: PGT145 antibody fragment, light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV / Envelope trimer / broadly neutralizing antibody / PGT145 / Cryo-EM / VIRAL PROTEIN
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsChatterjee A / Chen C / Lee K / Mangala Prasad V
Funding support United States, India, 3 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1126258 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI140868 United States
Other government India
CitationJournal: Npj Viruses / Year: 2023
Title: An HIV-1 broadly neutralizing antibody overcomes structural and dynamic variation through highly focused epitope targeting.
Authors: Hodge EA / Chatterjee A / Chen C / Naika GS / Laohajaratsang M / Mangala Prasad V / Lee KK
History
DepositionJun 21, 2023-
Header (metadata) releaseOct 25, 2023-
Map releaseOct 25, 2023-
UpdateOct 25, 2023-
Current statusOct 25, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36641.png

Downloads & links

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Map

FileDownload / File: emd_36641.map.gz / Format: CCP4 / Size: 32.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.72 Å
Density
Contour LevelBy AUTHOR: 0.021
Minimum - Maximum-0.14045447 - 0.16508593
Average (Standard dev.)0.00024466438 (±0.003280163)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions204204204
Spacing204204204
CellA=B=C: 350.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_36641_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_36641_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : BJOX2000.664 trimer in complex with broadly neutralizing HIV anti...

EntireName: BJOX2000.664 trimer in complex with broadly neutralizing HIV antibody PGT145
Components
  • Complex: BJOX2000.664 trimer in complex with broadly neutralizing HIV antibody PGT145
    • Protein or peptide: gp120 protein of HIV Envelope trimerEnvelope glycoprotein GP120
    • Protein or peptide: gp41 protein of HIV Envelope trimer
    • Protein or peptide: PGT145 antibody fragment, heavy chain
    • Protein or peptide: PGT145 antibody fragment, light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: BJOX2000.664 trimer in complex with broadly neutralizing HIV anti...

SupramoleculeName: BJOX2000.664 trimer in complex with broadly neutralizing HIV antibody PGT145
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: gp120 protein of HIV Envelope trimer

MacromoleculeName: gp120 protein of HIV Envelope trimer / type: protein_or_peptide / ID: 1
Details: The HIV trimer map of this study is of BJOX2000.664 but we have given a sequence of BG505.664 as the model of BG505.664 was used to rigid body fit in our map. Because of the low resolution ...Details: The HIV trimer map of this study is of BJOX2000.664 but we have given a sequence of BG505.664 as the model of BG505.664 was used to rigid body fit in our map. Because of the low resolution of the map, we have not built the model.
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 54.064277 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNNIT DDMRGELKNC SFNMTTELRD KKQKVYSLFY RLDVVQINEN QGNRSNNSNK E YRLINCNT ...String:
AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNNIT DDMRGELKNC SFNMTTELRD KKQKVYSLFY RLDVVQINEN QGNRSNNSNK E YRLINCNT SAITQACPKV SFEPIPIHYC APAGFAILKC KDKKFNGTGP CPSVSTVQCT HGIKPVVSTQ LLLNGSLAEE EV MIRSENI TNNAKNILVQ FNTPVQINCT RPNNNTRKSI RIGPGQAFYA TGDIIGDIRQ AHCNVSKATW NETLGKVVKQ LRK HFGNNT IIRFANSSGG DLEVTTHSFN CGGEFFYCNT SGLFNSTWIS NTSVQGSNST GSNDSITLPC RIKQIINMWQ RIGQ AMYAP PIQGVIRCVS NITGLILTRD GGSTNSTTET FRPGGGDMRD NWRSELYKYK VVKIEPLGVA PTRCKRRVVG RRRRR R

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Macromolecule #2: gp41 protein of HIV Envelope trimer

MacromoleculeName: gp41 protein of HIV Envelope trimer / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.146482 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEA QQHLLKLTVW GIKQLQARVL AVERYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALD

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Macromolecule #3: PGT145 antibody fragment, heavy chain

MacromoleculeName: PGT145 antibody fragment, heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.793164 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QASTMDWIWR ILFLVAAATS AHSQVQLVQS GAEVKKPGSS VKVSCKASGN SFSNHDVHWV RQATGQGLEW MGWMSHEGDK TGLAQKFQG RVTITRDSGA STVYMELRGL TADDTAIYYC LTGSKHRLRD YFLYNEYGPN YEEWGDYLAT LDVWGHGTAV T VSSASTKG ...String:
QASTMDWIWR ILFLVAAATS AHSQVQLVQS GAEVKKPGSS VKVSCKASGN SFSNHDVHWV RQATGQGLEW MGWMSHEGDK TGLAQKFQG RVTITRDSGA STVYMELRGL TADDTAIYYC LTGSKHRLRD YFLYNEYGPN YEEWGDYLAT LDVWGHGTAV T VSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE PVTVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LG TQTYICN VNHKPSNTKV DKKVEPKSCD

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Macromolecule #4: PGT145 antibody fragment, light chain

MacromoleculeName: PGT145 antibody fragment, light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.95375 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVVITQSPLF LPVTPGEAAS LSCKCSHSLQ HSTGANYLAW YLQRPGQTPR LLIHLATHRA SGVPDRFSGS GSGTDFTLKI SRVESDDVG TYYCMQGLHS PWTFGQGTKV EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV ...String:
EVVITQSPLF LPVTPGEAAS LSCKCSHSLQ HSTGANYLAW YLQRPGQTPR LLIHLATHRA SGVPDRFSGS GSGTDFTLKI SRVESDDVG TYYCMQGLHS PWTFGQGTKV EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV TEQDSKDSTY SLSSTLTLSK ADYEKHKVYA CEVTHQGLSS PVTKSFNRGE C

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Macromolecule #11: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 11 / Number of copies: 20 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridModel: EMS Lacey Carbon / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.75 µm
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 162.24 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

8643

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 667012
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5v8l


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsRigid body fitting followed by real space refinement to improve map occupancy
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8jtd:
BJOX2000.664 trimer in complex with Fab fragment of broadly neutralizing HIV antibody PGT145

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